From 7173caa9be4394e9a25b330dcaaa934ede768a05 Mon Sep 17 00:00:00 2001
From: Ming Yang <hustyangming@gmail.com>
Date: Mon, 14 Oct 2024 18:43:41 +0800
Subject: [PATCH] Fix styler issues.

---
 R/load_data.R                         | 42 +++++++++++++--------------
 R/load_rds.R                          | 16 +++++-----
 R/load_sas.R                          | 16 +++++-----
 R/load_xpt.R                          | 16 +++++-----
 R/utils.R                             |  8 ++---
 tests/testthat/setup.R                |  4 +--
 tests/testthat/test-data_integrity.R  | 18 ++++++------
 tests/testthat/test-default_dir.R     | 14 ++++-----
 tests/testthat/test-file_extensions.R | 12 ++++----
 tests/testthat/test-file_names.R      | 10 +++----
 tests/testthat/test-file_type.R       | 14 ++++-----
 tests/testthat/test-meta_data.R       | 22 +++++++-------
 tests/testthat/test-prefer_sas.R      | 18 ++++++------
 vignettes/integration-guide.Rmd       |  2 +-
 14 files changed, 106 insertions(+), 106 deletions(-)

diff --git a/R/load_data.R b/R/load_data.R
index 0d4194f..d9ac839 100644
--- a/R/load_data.R
+++ b/R/load_data.R
@@ -22,13 +22,13 @@
 #' @importFrom lifecycle deprecate_warn
 load_data <- function(sub_dir = NULL, file_names, use_wd = FALSE, prefer_sas = FALSE) {
   lifecycle::deprecate_warn("3.0.0", "load_data()", "read_data()")
-  
+
   if (is.null(file_names)) {
     stop("Usage: load_data: file_names: Must supply at least one file name")
   }
-  
+
   study_path <- "" # will be built using args
-  
+
   if (is.null(sub_dir)) {
     study_path <- getwd()
   } else {
@@ -38,10 +38,10 @@ load_data <- function(sub_dir = NULL, file_names, use_wd = FALSE, prefer_sas = F
       study_path <- file.path(get_cre_path(), sub_dir)
     }
   }
-  
+
   # create the output
   data_list <- create_data_list(study_path, file_names, prefer_sas) # nolint
-  
+
   return(data_list)
 }
 
@@ -75,39 +75,39 @@ create_data_list <- function(file_path, file_names, prefer_sas) {
     if (prefer_sas) {
       extensions <- c("", ".sas7bdat", ".rds")
     }
-    
+
     file_name_to_load <- NULL
-    
+
     candidates <- list.files(file_path)
     uppercase_candidates <- Map(toupper, candidates)
-    
+
     for (ext in extensions) {
       # Case insensitive file name match
       uppercase_file_name <- toupper(paste0(x, ext))
-      
+
       match_count <- sum(uppercase_candidates == uppercase_file_name)
       if (match_count > 1) {
         stop(paste("create_data_list(): More than one case-insensitive file name match for", file_path, x))
       }
-      
+
       index <- match(uppercase_file_name, uppercase_candidates)
       if (!is.na(index)) {
         file_name_to_load <- candidates[[index]]
         break
       }
     }
-    
+
     if (is.null(file_name_to_load)) {
       stop(paste("create_data_list(): No RDS or SAS files found for", file_path, x))
     }
-    
+
     output <- read_file(file_path, file_name_to_load)
-    
+
     return(output)
   })
-  
+
   names(data_list) <- file_names
-  
+
   return(data_list)
 }
 
@@ -118,29 +118,29 @@ create_data_list <- function(file_path, file_names, prefer_sas) {
 #' @return a data object with an extra attribute of metadata
 read_file <- function(file_path, file_name) {
   ext <- tools::file_ext(file_name)
-  
+
   if (!(toupper(ext) %in% c("RDS", "SAS7BDAT"))) {
     stop("Usage error: read_file: file_name: file must either be RDS or SAS7BDAT.")
   }
-  
+
   is_rds <- toupper(ext) == "RDS"
-  
+
   file <- file.path(file_path, file_name)
   file_name <- tools::file_path_sans_ext(file_name)
-  
+
   # grab file info
   meta <- file.info(file)[1L:6L]
   meta[["path"]] <- row.names(meta)
   meta[["file_name"]] <- file_name
   meta <- data.frame(meta, stringsAsFactors = FALSE)
   row.names(meta) <- NULL
-  
+
   if (is_rds) {
     out <- readRDS(file)
   } else {
     out <- haven::read_sas(file)
   }
   attr(out, "meta") <- meta
-  
+
   return(out)
 }
diff --git a/R/load_rds.R b/R/load_rds.R
index a1a9008..8211564 100644
--- a/R/load_rds.R
+++ b/R/load_rds.R
@@ -9,37 +9,37 @@
 #' temp_dir <- tempdir()
 #' adsl_rds_file <- file.path(temp_dir, "adsl.rds")
 #' adae_rds_file <- file.path(temp_dir, "adae.rds")
-#' 
+#'
 #' # Write example data to RDS files
 #' saveRDS(pharmaverseadam::adsl, adsl_rds_file)
 #' saveRDS(pharmaverseadam::adae, adae_rds_file)
-#' 
+#'
 #' # Load RDS files
 #' rds_data_list <- load_rds(c(adsl_rds_file, adae_rds_file))
-#' 
+#'
 #' # Clean up
 #' unlink(c(adsl_rds_file, adae_rds_file))
 #' @export
 load_rds <- function(files) {
   # Check if files is a character vector
   checkmate::assert_character(files)
-  
+
   # Read each file and add metadata
   data_list <- lapply(files, function(file) {
     # Check if file exists
     checkmate::assert_file_exists(file)
     # Check if file is an RDS file
     check_file_ext(file, extension = "rds")
-    
+
     # Read RDS file
     data <- readRDS(file)
-    
+
     # Get file info and add to data as an attribute
     attr(data, "meta") <- file_info(file)
-    
+
     return(data)
   })
-  
+
   # Set names of data_list to the file names
   names(data_list) <- basename(files)
 
diff --git a/R/load_sas.R b/R/load_sas.R
index 01c7a4c..5707afa 100644
--- a/R/load_sas.R
+++ b/R/load_sas.R
@@ -9,37 +9,37 @@
 #' temp_dir <- tempdir()
 #' adsl_sas_file <- file.path(temp_dir, "adsl.sas7bdat")
 #' adae_sas_file <- file.path(temp_dir, "adae.sas7bdat")
-#' 
+#'
 #' # Write example data to SAS files
 #' haven::write_sas(pharmaverseadam::adsl, adsl_sas_file)
 #' haven::write_sas(pharmaverseadam::adae, adae_sas_file)
-#' 
+#'
 #' # Load SAS files
 #' sas_data_list <- load_sas(c(adsl_sas_file, adae_sas_file))
-#' 
+#'
 #' # Clean up
 #' unlink(c(adsl_sas_file, adae_sas_file))
 #' @export
 load_sas <- function(files) {
   # Check if files is a character vector
   checkmate::assert_character(files)
-  
+
   # Read each file and add metadata
   data_list <- lapply(files, function(file) {
     # Check if file exists
     checkmate::assert_file_exists(file)
     # Check if file is a SAS file
     check_file_ext(file, extension = "sas7bdat")
-        
+
     # Read SAS file
     data <- haven::read_sas(file)
-    
+
     # Get file info and add to data as an attribute
     attr(data, "meta") <- file_info(file)
-    
+
     return(data)
   })
-  
+
   # Set names of data_list to the file names
   names(data_list) <- basename(files)
   return(data_list)
diff --git a/R/load_xpt.R b/R/load_xpt.R
index debf34b..2c8644e 100644
--- a/R/load_xpt.R
+++ b/R/load_xpt.R
@@ -9,16 +9,16 @@
 #' temp_dir <- tempdir()
 #' adsl_xpt_file <- file.path(temp_dir, "adsl.xpt")
 #' adae_xpt_file <- file.path(temp_dir, "adae.xpt")
-#' 
+#'
 #' # Write example data to XPT files
 #' haven::write_xpt(pharmaverseadam::adsl, adsl_xpt_file)
 #' haven::write_xpt(pharmaverseadam::adae, adae_xpt_file)
-#' 
+#'
 #' # Load XPT files
 #' xpt_data_list <- load_xpt(c(adsl_xpt_file, adae_xpt_file))
-#' 
+#'
 #' # Clean up
-#' unlink(c(adsl_xpt_file, adae_xpt_file))  
+#' unlink(c(adsl_xpt_file, adae_xpt_file))
 #' @export
 load_xpt <- function(files) {
   # Check if files is a character vector
@@ -30,16 +30,16 @@ load_xpt <- function(files) {
     checkmate::assert_file_exists(file)
     # Check if file is an XPT file
     check_file_ext(file, extension = "xpt")
-    
+
     # Read XPT file
     data <- haven::read_xpt(file)
-    
+
     # Get file info and add to data as an attribute
     attr(data, "meta") <- file_info(file)
-    
+
     return(data)
   })
-  
+
   # Set names of data_list to the file names
   names(data_list) <- basename(files)
 
diff --git a/R/utils.R b/R/utils.R
index 6204502..01fa560 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -9,7 +9,7 @@ check_file_ext <- function(file, extension) {
   # Check input types
   checkmate::assert_string(file)
   checkmate::assert_string(extension)
-  
+
   # Extract file extension (case-insensitive)
   file_ext <- tolower(tools::file_ext(file))
 
@@ -18,7 +18,7 @@ check_file_ext <- function(file, extension) {
 
   # Check that the file extension is one of the allowed choices
   checkmate::assert_choice(file_ext, choices = c("rds", "sas7bdat", "xpt"))
-  
+
   # Compare with the given extension (case-insensitive)
   return(file_ext == tolower(extension))
 }
@@ -39,7 +39,7 @@ file_info <- function(file) {
 
   # Get the path from the rownames
   path <- rownames(info)
-  
+
   # Check file and path are the same
   checkmate::assert_true(file == path)
 
@@ -49,7 +49,7 @@ file_info <- function(file) {
 
   # Convert to list to remove row names
   info <- as.list(info)
-    
+
   # Return the file information as a list
   return(info)
 }
diff --git a/tests/testthat/setup.R b/tests/testthat/setup.R
index ac6ce9e..1580a08 100644
--- a/tests/testthat/setup.R
+++ b/tests/testthat/setup.R
@@ -47,7 +47,7 @@ Sys.setenv(RXD_DATA = temp_dir)
 # Load RDS data via load_data()
 lifecycle::expect_deprecated(
   iris_data_rds <- dv.loader::load_data(
-    sub_dir = ".", 
+    sub_dir = ".",
     file_names = "iris.rds"
   )
 )
@@ -55,7 +55,7 @@ lifecycle::expect_deprecated(
 # Load SAS data via load_data()
 lifecycle::expect_deprecated(
   iris_data_sas <- dv.loader::load_data(
-    sub_dir = ".", 
+    sub_dir = ".",
     file_names = "iris.sas7bdat"
   )
 )
diff --git a/tests/testthat/test-data_integrity.R b/tests/testthat/test-data_integrity.R
index f845987..38f37f4 100644
--- a/tests/testthat/test-data_integrity.R
+++ b/tests/testthat/test-data_integrity.R
@@ -1,17 +1,17 @@
 test_that(
   desc = vdoc[["add_spec"]](
-    desc = "Ensures that the data integrity is maintained across different file types and loading methods, 
+    desc = "Ensures that the data integrity is maintained across different file types and loading methods,
     comparing the loaded data against a known reference dataset.",
     spec = specs$data_integrity
-  ), 
-  code = { 
+  ),
+  code = {
     # load_data(): check that the RDS file is loaded correctly
     expect_equal(
       object = iris_data_rds[["iris.rds"]],
       expected = iris_data,
       ignore_attr = TRUE
     )
-    
+
     # load_data(): check that the SAS file is loaded correctly
     expect_equal(
       object = iris_data_sas[["iris.sas7bdat"]],
@@ -21,21 +21,21 @@ test_that(
 
     # load_rds(): check that the RDS file is loaded correctly
     expect_equal(
-      object = iris_rds[["iris.rds"]], 
+      object = iris_rds[["iris.rds"]],
       expected = iris_data,
       ignore_attr = TRUE
     )
-    
+
     # load_sas(): check that the SAS file is loaded correctly
     expect_equal(
-      object = iris_sas[["iris.sas7bdat"]], 
+      object = iris_sas[["iris.sas7bdat"]],
       expected = iris_data,
       ignore_attr = TRUE
     )
-    
+
     # load_xpt(): check that the XPT file is loaded correctly
     expect_equal(
-      object = iris_xpt[["iris.xpt"]], 
+      object = iris_xpt[["iris.xpt"]],
       expected = iris_data,
       ignore_attr = TRUE
     )
diff --git a/tests/testthat/test-default_dir.R b/tests/testthat/test-default_dir.R
index d9e8a12..44bea9d 100644
--- a/tests/testthat/test-default_dir.R
+++ b/tests/testthat/test-default_dir.R
@@ -1,23 +1,23 @@
-test_that(  
+test_that(
   desc = vdoc[["add_spec"]](
-    desc = "Verifies that load_data() can correctly locate and load data files using 
+    desc = "Verifies that load_data() can correctly locate and load data files using
     relative paths from the current working directory.",
     spec = specs$default_dir
-  ), 
+  ),
   code = {
     # Save the current working directory
     old_wd <- getwd()
-    
+
     # Change the working directory to the temporary directory
     setwd(temp_dir)
-    
+
     lifecycle::expect_deprecated(
       # load_data(): load the RDS file with use_wd = TRUE
       data1 <- dv.loader::load_data(
         sub_dir = ".",
         file_names = "iris.rds",
         use_wd = TRUE
-      )    
+      )
     )
 
     lifecycle::expect_deprecated(
@@ -26,7 +26,7 @@ test_that(
         sub_dir = ".",
         file_names = "iris.sas7bdat",
         use_wd = TRUE
-      )      
+      )
     )
 
     # Expect that the RDS file is loaded
diff --git a/tests/testthat/test-file_extensions.R b/tests/testthat/test-file_extensions.R
index dd9a6dd..da53f60 100644
--- a/tests/testthat/test-file_extensions.R
+++ b/tests/testthat/test-file_extensions.R
@@ -2,27 +2,27 @@ test_that(
   desc = vdoc[["add_spec"]](
     desc = "appropriate error messages are thrown when attempting to load or read files without valid extensions",
     spec = specs$file_extensions
-  ), 
+  ),
   code = {
     # load_data(): load data with no file extension
     lifecycle::expect_deprecated(
       dv.loader::load_data(sub_dir = ".", file_names = "iris")
     ) |>
       expect_error("file must either be RDS or SAS7BDAT")
-    
+
     # Expected error message
     error_msg <- "Assertion on 'file_ext != \"\"' failed: Must be TRUE."
 
     # load_rds(): expect an error when the file extension is empty
-    dv.loader::load_rds(files = iris_file) |> 
-      expect_error(error_msg) 
+    dv.loader::load_rds(files = iris_file) |>
+      expect_error(error_msg)
 
     # load_sas(): expect an error when the file extension is empty
-    dv.loader::load_sas(files = iris_file) |> 
+    dv.loader::load_sas(files = iris_file) |>
       expect_error(error_msg)
 
     # load_xpt(): expect an error when the file extension is empty
-    dv.loader::load_xpt(files = iris_file) |> 
+    dv.loader::load_xpt(files = iris_file) |>
       expect_error(error_msg)
   }
 )
diff --git a/tests/testthat/test-file_names.R b/tests/testthat/test-file_names.R
index 4212ae9..7e8066f 100644
--- a/tests/testthat/test-file_names.R
+++ b/tests/testthat/test-file_names.R
@@ -2,23 +2,23 @@ test_that(
   desc = vdoc[["add_spec"]](
     desc = "appropriate error messages are thrown when the required 'file_names' argument is not provided",
     spec = specs$file_names
-  ), 
+  ),
   code = {
     lifecycle::expect_deprecated(
-     # load_data(): expect an error when the file_names argument is missing
+      # load_data(): expect an error when the file_names argument is missing
       load_data(sub_dir = ".")
     ) |>
       expect_error('argument "file_names" is missing, with no default')
-    
+
     # Expected error message
     error_msg <- 'argument "files" is missing, with no default'
 
     # load_rds(): expect an error when the files argument is missing
     expect_error(dv.loader::load_rds(), error_msg)
-    
+
     # load_sas(): expect an error when the files argument is missing
     expect_error(dv.loader::load_sas(), error_msg)
-    
+
     # load_xpt(): expect an error when the files argument is missing
     expect_error(dv.loader::load_xpt(), error_msg)
   }
diff --git a/tests/testthat/test-file_type.R b/tests/testthat/test-file_type.R
index b77411e..6489118 100644
--- a/tests/testthat/test-file_type.R
+++ b/tests/testthat/test-file_type.R
@@ -1,25 +1,25 @@
 test_that(
   desc = vdoc[["add_spec"]](
-    desc = "appropriate error messages are thrown when attempting to load or 
+    desc = "appropriate error messages are thrown when attempting to load or
     read file with types that are not supported.",
     spec = specs$file_type
-  ), 
-  code = {   
+  ),
+  code = {
     # load_data(): expect an error when the file type is not supported
     lifecycle::expect_deprecated(
       dv.loader::load_data(sub_dir = ".", file_names = "iris.txt")
     ) |>
       expect_error("file must either be RDS or SAS7BDAT")
-    
+
     # Expected error message
     error_msg <- "Must be element of set \\{'rds','sas7bdat','xpt'\\}, but is 'txt'."
-    
+
     # load_rds(): expect an error when the file extension is not supported
     expect_error(dv.loader::load_rds(files = iris_txt_file), error_msg)
-    
+
     # load_sas(): expect an error when the file extension is not supported
     expect_error(dv.loader::load_sas(files = iris_txt_file), error_msg)
-    
+
     # load_xpt(): expect an error when the file extension is not supported
     expect_error(dv.loader::load_xpt(files = iris_txt_file), error_msg)
   }
diff --git a/tests/testthat/test-meta_data.R b/tests/testthat/test-meta_data.R
index 126862d..8f27d8a 100644
--- a/tests/testthat/test-meta_data.R
+++ b/tests/testthat/test-meta_data.R
@@ -1,6 +1,6 @@
 test_that(
   desc = vdoc[["add_spec"]](
-    desc = "load_data(), load_rds(), load_sas(), and load_xpt() functions correctly extract and 
+    desc = "load_data(), load_rds(), load_sas(), and load_xpt() functions correctly extract and
     attach metadata of the file to the loaded data",
     spec = specs$meta_data
   ),
@@ -9,34 +9,34 @@ test_that(
     rds_file_info <- file.info(iris_rds_file, extra_cols = FALSE)
     sas_file_info <- file.info(iris_sas_file, extra_cols = FALSE)
     xpt_file_info <- file.info(iris_xpt_file, extra_cols = FALSE)
-    
+
     # load_data(): check metadata for RDS file
     expect_equal(
-      as.list(attr(iris_data_rds[["iris.rds"]], "meta")[names(rds_file_info)]), 
+      as.list(attr(iris_data_rds[["iris.rds"]], "meta")[names(rds_file_info)]),
       as.list(rds_file_info)
     )
-    
+
     # load_data(): check metadata for SAS file
     expect_equal(
-      as.list(attr(iris_data_sas[["iris.sas7bdat"]], "meta")[names(sas_file_info)]), 
+      as.list(attr(iris_data_sas[["iris.sas7bdat"]], "meta")[names(sas_file_info)]),
       as.list(sas_file_info)
     )
-    
+
     # load_rds(): check metadata for RDS file
     expect_equal(
-      as.list(attr(iris_rds[["iris.rds"]], "meta")[names(rds_file_info)]), 
+      as.list(attr(iris_rds[["iris.rds"]], "meta")[names(rds_file_info)]),
       as.list(rds_file_info)
     )
-    
+
     # load_sas(): check metadata for SAS file
     expect_equal(
-      as.list(attr(iris_sas[["iris.sas7bdat"]], "meta")[names(sas_file_info)]), 
+      as.list(attr(iris_sas[["iris.sas7bdat"]], "meta")[names(sas_file_info)]),
       as.list(sas_file_info)
     )
-    
+
     # load_xpt(): check metadata for XPT file
     expect_equal(
-      as.list(attr(iris_xpt[["iris.xpt"]], "meta")[names(xpt_file_info)]), 
+      as.list(attr(iris_xpt[["iris.xpt"]], "meta")[names(xpt_file_info)]),
       as.list(xpt_file_info)
     )
   }
diff --git a/tests/testthat/test-prefer_sas.R b/tests/testthat/test-prefer_sas.R
index 837ba34..5174432 100644
--- a/tests/testthat/test-prefer_sas.R
+++ b/tests/testthat/test-prefer_sas.R
@@ -2,35 +2,35 @@ test_that(
   desc = vdoc[["add_spec"]](
     desc = "load_data() loads the RDS file if prefer_sas is FALSE, and it loads the SAS file if prefer_sas is TRUE.",
     spec = specs$prefer_sas
-  ), 
+  ),
   code = {
     # load_data(): load the RDS file with prefer_sas = FALSE
     lifecycle::expect_deprecated(
       data_rds <- dv.loader::load_data(
         sub_dir = ".",
         file_names = "iris.rds",
-        prefer_sas = FALSE 
+        prefer_sas = FALSE
       )
     )
-    
+
     # load_data(): load the SAS file with prefer_sas = TRUE
     lifecycle::expect_deprecated(
       data_sas <- load_data(
-        sub_dir = ".", 
+        sub_dir = ".",
         file_names = "iris.sas7bdat",
         prefer_sas = TRUE
       )
     )
-    
+
     # Get metadata for RDS file
     meta_rds <- attr(data_rds[["iris.rds"]], "meta")
-    
+
     # Get metadata for SAS file
     meta_sas <- attr(data_sas[["iris.sas7bdat"]], "meta")
-    
+
     # Check if the correct RDS file is loaded
-    expect_equal(basename(meta_rds[["path"]]), "iris.rds")  
-    
+    expect_equal(basename(meta_rds[["path"]]), "iris.rds")
+
     # Check if the correct file is loaded
     expect_equal(basename(meta_sas[["path"]]), "iris.sas7bdat")
   }
diff --git a/vignettes/integration-guide.Rmd b/vignettes/integration-guide.Rmd
index f6393de..95a8e0f 100644
--- a/vignettes/integration-guide.Rmd
+++ b/vignettes/integration-guide.Rmd
@@ -66,7 +66,7 @@ Execute the `dv.manager::run_app()` function to initiate the DaVinci application
 ```{r, eval=FALSE}
 # Run the DaVinci application with data and module lists defined earlier
 dv.manager::run_app(
-  data = list("pharmaverseadam" = data_list), 
+  data = list("pharmaverseadam" = data_list),
   module_list = module_list,
   filter_data = "adsl",
   title = "DaVinci Application"